1 #summary Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby -- under development!
9 Tutorial for multiple sequence alignments and phylogenetic methods in [http://bioruby.open-bio.org/ BioRuby].
11 Eventually, this is expected to be placed on the official !BioRuby page.
13 Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
16 Copyright (C) 2011 Christian M Zmasek. All rights reserved.
19 = Multiple Sequence Alignment =
22 == Multiple Sequence Alignment Input and Output ==
24 === Reading in a Multiple Sequence Alignment from a File ===
26 The following example shows how to read in a *ClustalW*-formatted multiple sequence alignment.
32 # Reads in a ClustalW-formatted multiple sequence alignment
33 # from a file named "infile_clustalw.aln" and stores it in 'report'.
34 report = Bio::ClustalW::Report.new(File.read('infile_clustalw.aln'))
36 # Accesses the actual alignment.
37 msa = report.alignment
39 # Goes through all sequences in 'msa' and prints the
40 # actual molecular sequence.
48 === Writing a Multiple Sequence Alignment to a File ===
51 The following example shows how to write a multiple sequence alignment in *FASTA*-format. It first creates a file named "outfile.fasta" for writing ('w') and then writes the multiple sequence alignment referred to by variable 'msa' to it in FASTA-format (':fasta').
57 # Creates a new file named "outfile.fasta" and writes
58 # multiple sequence alignment 'msa' to it in fasta format.
59 File.open('outfile.fasta', 'w') do |f|
60 f.write(msa.output(:fasta))
64 ==== Setting the Output Format ====
66 The following symbols determine the output format:
68 * `:clustal` for ClustalW
70 * `:phylip`for PHYLIP interleaved (will truncate sequence names to no more than 10 characters)
71 * `:phylipnon` for PHYLIP non-interleaved (will truncate sequence names to no more than 10 characters)
73 * `:molphy` for Molphy
76 For example, the following writes in PHYLIP's non-interleaved format:
79 f.write(align.output(:phylipnon))
83 === Formatting of Individual Sequences ===
87 !BioRuby can format molecular sequences in a variety of formats.
88 Individual sequences can be formatted to (e.g.) Genbank format as shown in the following examples.
92 seq.to_seq.output(:genbank)
95 For Bio::!FlatFile entries:
97 entry.to_biosequence.output(:genbank)
100 The following symbols determine the output format.
101 *`:genbank` for Genbank
104 == Calculating Multiple Sequence Alignments ==
106 !BioRuby can be used to execute a variety of multiple sequence alignment
107 programs (such as [http://mafft.cbrc.jp/alignment/software/ MAFFT], [http://probcons.stanford.edu/ Probcons], [http://www.clustal.org/ ClustalW], [http://www.drive5.com/muscle/ Muscle], and [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html T-Coffee]).
108 In the following, examples for using the MAFFT and Muscle are shown.
113 The following example uses the MAFFT program to align four sequences
114 and then prints the result to the screen.
115 Please note that if the path to the MAFFT executable is properly set `mafft=Bio::MAFFT.new(options)` can be used instead of explicitly indicating the path as in the example.
121 # 'seqs' is either an array of sequences or a multiple sequence
122 # alignment. In general this is read in from a file as described in ?.
123 # For the purpose of this tutorial, it is generated in code.
124 seqs = ['MFQIPEFEPSEQEDSSSAER',
125 'MGTPKQPSLAPAHALGLRKS',
130 # Calculates the alignment using the MAFFT program on the local
131 # machine with options '--maxiterate 1000 --localpair'
132 # and stores the result in 'report'.
133 options = ['--maxiterate', '1000', '--localpair']
134 mafft = Bio::MAFFT.new('path/to/mafft', options)
135 report = mafft.query_align(seqs)
137 # Accesses the actual alignment.
138 align = report.alignment
140 # Prints each sequence to the console.
141 align.each { |s| puts s.to_s }
147 * Katoh, Toh (2008) "Recent developments in the MAFFT multiple sequence alignment program" Briefings in Bioinformatics 9:286-298
149 * Katoh, Toh 2010 (2010) "Parallelization of the MAFFT multiple sequence alignment program" Bioinformatics 26:1899-1900
159 # 'seqs' is either an array of sequences or a multiple sequence
160 # alignment. In general this is read in from a file as described in ?.
161 # For the purpose of this tutorial, it is generated in code.
162 seqs = ['MFQIPEFEPSEQEDSSSAER',
163 'MGTPKQPSLAPAHALGLRKS',
167 # Calculates the alignment using the Muscle program on the local
168 # machine with options '-quiet -maxiters 64'
169 # and stores the result in 'report'.
170 options = ['-quiet', '-maxiters', '64']
171 muscle = Bio::Muscle.new('path/to/muscle', options)
172 report = muscle.query_align(seqs)
174 # Accesses the actual alignment.
175 align = report.alignment
177 # Prints each sequence to the console.
178 align.each { |s| puts s.to_s }
184 * Edgar, R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput" Nucleic Acids Res 32(5):1792-1797
186 === Other Programs ===
188 _need more detail here..._
190 [http://probcons.stanford.edu/ Probcons], [http://www.clustal.org/ ClustalW], and [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html T-Coffee] can be used in the same manner as the programs above.
194 == Manipulating Multiple Sequence Alignments ==
196 Oftentimes, multiple sequence to be used for phylogenetic inference are 'cleaned up' in some manner. For instance, some researchers prefer to delete columns with more than 50% gaps. The following code is an example of how to do that in !BioRuby.
210 = Phylogenetic Trees =
213 == Phylogenetic Tree Input and Output ==
216 === Reading in of Phylogenetic Trees ===
220 ====Newick or New Hampshire Format====
230 ====phyloXML Format====
232 Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
234 In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command:
237 % gem install -r libxml-ruby
240 This example reads file "example.xml" and stores its [http://www.phyloxml.org/ phyloXML]-formatted trees in variable 'trees'.
246 # This creates new phyloXML parser.
247 trees = Bio::PhyloXML::Parser.new('example.xml')
249 # This prints the names of all trees in the file.
254 # If there are several trees in the file, you can access the one you wish via index.
270 === Writing of Phylogenetic Trees ===
272 ====Newick or New Hampshire Format====
282 ====phyloXML Format====
284 Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
286 In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command:
289 % gem install -r libxml-ruby
292 This example writes trees 'tree1' and 'tree2' to file "tree.xml" in [http://www.phyloxml.org/ phyloXML] format.
298 # this creates new phyloXML writer.
299 writer = Bio::PhyloXML::Writer.new('tree.xml')
301 # Writes tree to the file "tree.xml".
304 # Adds another tree to the file.
322 = Phylogenetic Inference =
324 _Currently !BioRuby does not contain wrappers for phylogenetic inference programs, thus I am progress of writing a RAxML wrapper followed by a wrapper for FastME..._
326 == Optimality Criteria Based on Character Data ==
328 Character data based methods work directly on molecular sequences and thus do not require the calculation of pairwise distances but tend to be time consuming and sensitive to errors in the multiple sequence alignment.
330 === Maximum Likelihood ===
353 === Maximum Parsimony ===
355 Currently no direct support in !BioRuby.
358 === Bayesian Inference ===
360 Currently no direct support in !BioRuby.
363 == Pairwise Distance Based Methods ==
365 === Pairwise Sequence Distance Estimation ===
376 === Optimality Criteria Based on Pairwise Distances ===
379 ==== Minimal Evolution: FastME ====
389 === Algorithmic Methods Based on Pairwise Distances ===
391 ==== Neighbor Joining and Related Methods ====
407 == Support Calculation? ==
409 === Bootstrap Resampling? ===
414 = Analyzing Phylogenetic Trees =
419 == Gene Duplication Inference ==
421 _need to further test and then import GSoC 'SDI' work..._
429 = Putting It All Together =
431 Example of a small "pipeline"-type program running a mininal phyogenetic analysis: starting with a set of sequences and ending with a phylogenetic tree.